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Publications

2013 - 34 publications

Banisch, Ralf and Hartmann, C. (2013) Meshless discretization of LQ-type stochastic control problems. arXiv preprint, arXiv: . (Unpublished)

Bruckner, S. and Hüffner, F. and Komusiewicz, Ch. and Niedermeier, R. (2013) Evaluation of ILP-based approaches for partitioning into colorful components. In: Experimental Algorithms. Lecture Notes in Computer Science, 7933 (7933). Springer, Heidelberg, pp. 176-187. ISBN 978-3-642-38526-1 (print) / 978-3-642-38527-8 (online)

Bruckner, S. and Kayser, B. and Conrad, T. O. F. (2013) Finding Modules in Networks with Non-modular Regions. Lecture Notes in Computer Science (Proceedings of SEA 2013), 7933 . pp. 188-199. ISSN 0302-9743

Delle Site, L. (2013) Multidisziplinarität in Deutschland: Mehrwert oder Beschränkung? Physik Journal (12). p. 17.

Delle Site, L. and Ghiringhelli, L. M. and Ceperley, D.M. (2013) Electronic Energy Functionals: Levy-Lieb principle within the Ground State Path Integral Quantum Monte Carlo. International Journal of Quantum Chemistry, 113 . p. 155.

Enciso , M. and Schütte, Ch. and Delle Site, L. (2013) pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study. Molecular Physics, 111 (22-23). pp. 3363-3371. ISSN 0026-8976

Enciso , M. and Schütte, Ch. and Delle Site, L. (2013) pH-dependent coarse-grained model of peptides. Soft Matter, 9 (26). pp. 6118-6127.

Gul, Rahim and Bernhard, Stefan (2013) Local sensitivity analysis of cardiovascular system parameters. International Journal of Scientific and Engineering Research (IJSER), 4 (7). pp. 2648-2661. ISSN 2229-5518

Gupta, Pooja and Reinsch , Norbert and Spötter, Andreas and Conrad, T. O. F. and Bienefeld, Kaspar (2013) Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera). BMC Genetics, 14 (36).

Haack, F. and Fackeldey, K. and Röblitz, S. and Scharkoi, O. and Weber, M. and Schmidt, B. (2013) Adaptive spectral clustering with application to tripeptide conformation analysis. J. Chem. Phys., 139 (19). p. 194110.

Hartmann, C. and Banisch, Ralf and Sarich, M. and Badowski, T. and Schütte, Ch. (2013) Characterization of Rare Events in Molecular Dynamics. Entropy (Special Issue), 16 (1). pp. 350-376. ISSN 1099-4300

Hartmann, C. and Schäfer-Bung, B. and Thöns-Zueva, A. (2013) Balanced averaging of bilinear systems with applications to stochastic control. SIAM J. Control Optim., 51 (3). pp. 2356-2378.

Hartmann, C. and Yanao, Tomohiro (2013) The falling cat problem and shape effects in small molecules in a random environment: a case study. Molecular Physics, 111 (22-23). pp. 3534-3545. ISSN 0026-8976

Latorre, J.C. and Pavliotis, G. A. and Kramer, P. R. (2013) Corrections to Einstein's relation for Brownian motion in a tilted periodic potential. J. Stat. Phys., 150 (4). pp. 776-803. ISSN 0022-4715

Lie, Han Cheng and Fackeldey, Konstantin and Weber, Marcus (2013) A Square Root Approximation of Transition Rates for a Markov State Model. SIAM Journal on Matrix Analysis and Applications, 34 (2). p. 738. ISSN 0895-4798

Nikitin, A. and Wulkow, M. and Schütte, Ch. (2013) Modeling of Free Radical Styrene/Divinylbenzene Copolymerization with the Numerical Fractionation Technique. Macromolecular Theory and Simulation, 22 (9). pp. 475-489.

Noé, F. and Nüske, F. (2013) A variational approach to modeling slow processes in stochastic dynamical systems. SIAM Multiscale Model. Simul., 11 . pp. 635-655.

Paulus, F. and Weiss, M. E. R. and Steinhilber, D. and Nikitin, A. and Schütte, Ch. and Haag, R. (2013) Anionic Ring-Opening Polymerization Simulations for Hyperbranched Polyglycerols with Defined Molecular Weights. Macromolecules, 46 (21). pp. 8458-8466. ISSN 0024-9297

Peuker, Sebastian and Cukkemane, Abhishek and Held, M. and Noé, F. and Kaupp, Benjamin and Seifert, Reinhard (2013) Kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein. Biophys. J., 104 . pp. 63-74.

Pluharova, E. and Marsalek, O. and Schmidt, B. and Jungwirth, P. (2013) Ab Initio Molecular Dynamics Approach to Quantitative Description of Ion Pairing in Water. J. Phys. Chem. Lett., 4 (23). pp. 4177-4181.

Pérez-Hernández, G. and Paul, F. and Giorgino, T. and de Fabritiis, G. and Noé, F. (2013) Identification of slow molecular order parameters for Markov model construction. J. Chem. Phys., 139 . 015102.

Pérez-Hernández, G. and Schmidt, B. (2013) Anisotropy of the Water-Carbon Interaction: Molecular Simulations of Water in Low-Diameter Carbon Nano-Tubes. Phys. Chem. Chem. Phys., 15 (14). pp. 4995-5006.

Rath, B. A. and Yousef, K. P. and Katzenstein, D. K. and Shafer, R. W. and Schütte, Ch. and von Kleist, M. and Merigan, T. C. (2013) In vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis. PLoS ONE, 8 (4). e61102. ISSN 1932-6203

Rath , B. and Tief, F. and Karsch, K. and Muehlhans, S. and Obermeier, P. and Adamou, E. and Chen, X. and Seeber, L. and Peiser, Ch. and Hoppe, Ch. and von Kleist, M. and Conrad, T. O. F. and Schweiger, B. (2013) Towards a personalized approach to managing of influenza infections in infants and children - food for thought and a note on oseltamivir. Infectious Disorders - Drug Targets, 13 (1). pp. 25-33. ISSN 2212-3989

Rath, B. and von Kleist, M. and Castillo, M. E. and Kolevic, L. and Caballero, P. and Soto-Castellares, G. and Amedee, A. M. and Robinson, J.E. and Katzenstein, D. K. and Van Dyke, R.B. and Oberhelman, R. (2013) Antiviral Resistance and Correlates of Virologic Failure in the first Cohort of HIV-Infected Children Gaining Access to Structured Antiretroviral Therapy in Lima, Peru: A Cross-Sectional Analysis. BMC Infectious Diseases, 13 (1).

Sarich, M. and Banisch, Ralf and Hartmann, C. and Schütte, Ch. (2013) Markov State Models for Rare Events in Molecular Dynamics. Entropy (Special Issue), 16 (1). pp. 258-286. ISSN 1099-4300

Schmidt, B. and Lorenz, U. (2013) WavePacket 4.9: A Matlab program package for quantum-mechanical wavepacket propagation and time-dependent spectroscopy. Freely available at SourceForge.net.

Schöneberg, J. and Noé, F. (2013) ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments. PLoS ONE, 8 . e74261. ISSN 1932-6203

Schütte, Ch. and Sarich, M. (2013) Metastability and Markov State Models in Molecular Dynamics: Modeling, Analysis, Algorithmic Approaches. Courant Lecture Notes, 24 . American Mathematical Society. ISBN 0821843591

Steger, Katrin and Bollmann, Stefan and Noé, F. and Doose, S. (2013) Systematic evaluation of fluorescence correlation spectroscopy data analysis on the nanosecond time scale. Phys. Chem. Chem. Phys., 15 . pp. 10435-10445.

Trendelkamp-Schroer, B. and Noé, F. (2013) Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution. J. Phys. Chem., 138 . p. 164113.

Wang, H. and Hartmann, C. and Schütte, Ch. (2013) Linear response theory and optimal control for a molecular system under nonequilibrium conditions. Molecular Physics, 111 . pp. 3555-3564. ISSN 0026-8976

Wang, H. and Hartmann, C. and Schütte, Ch. and Delle Site, L. (2013) Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique. Phys. Rev. X, 3 . 011018.

Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2013) Markov Control Processes with Rare State Observation: Sensitivity Analysis with Respect to Optimal Treatment Strategies against HIV-1. International Journal of Biomathematics and Biostatistics, 2 (1). ISSN 0973-7340